Story: This is Robotnik's latest scheme to rid Mobius of everything that is considered good. Robotnik created a machine to turn the care-free beans that live in Beanville into robotic slaves. His robots are sent to collect the beans.

Levels: There are a total of 13 stages: stages 1 to 12 are against robots (Arms, Frankly, Humpty, Coconuts, Davy Sprocket, Skweel, Dynamight, Grounder, Spike, Sir Ffuzzy-Logik, Dragon Breath, and Scratch), and the 13th stage is fought against Robotnik.

Chaos Emeralds: There are no Chaos Emeralds in this game.

Miscellaneous: At first the game seems to be simple. Two beans will fall from the top of the screen. The player can rotate the beans in any direction until they fall to the ground. If four beans of the same color touch each other, they will be freed. Beans can also be freed in combos. For example, suppose that freeing four pink beans causes four purple beans to become free-this creates a combo. Performing these combos can send refugee beans to the opponent.

The game becomes more challenging with the addition of refugee beans. Refugee beans cannot be grouped like other colorful beans. Instead, they must escape with a group of colorful beans. It is better to give than to receive, so it is important to free beans in combinations so that your opponent will become overwhelmed with refugee beans. When new beans cannot fall onto the screen, the game is over.

There are three different modes of play in Dr. Robotnik's Mean Bean Machine. The first mode is Scenario Mode, where the opponent is one of Robotnik's robots. By default the difficulty is normal. However, by going to Options you can change the difficulty. There are four difficulty levels: Easy, Normal, Hard, and Hardest. The story does not change based on the difficulty level, but there is a message at the end of the game telling you to try the next difficulty level. (On Hardest mode the message thanks you for playing.)

In 1P vs. 2P Mode, two humans can challenge each other. The difficulty of each player can be set at the beginning of each match. If the difficulty is set to Hard or Hardest, the player will start with a handicap: rows of refugee beans will drop from the screen before the colorful beans will come down.

The final mode, Exercise Mode, allows one or two players to improve their skills by practicing. No refugee beans exist in this mode. However, there are a couple of extra beans. A Big Bean (a large green bean) will come down as a playable bean. Big Bean is so heavy that it gets rid of two columns of beans. Has Bean (who usually stands by the score) can also come into play, turning beans all of the same color as he moves down the screen.

As a side note, when the title screen appears on the screen (and press start is flashing), you can press up, A, B, or C to make the beans spelling "Mean Bean" jump. The first player controller can make the word "Mean" jump, while the second player controller can make the word "Bean" jump.

There is another version of Dr. Robotnik's Mean Bean Machine available on the Game Gear. The main difference is the addition of Puzzle Mode.